As an apparatus for heat-treating a substrate, one is known in which a heating plate is arranged at the lower portion of a vacuum chamber, an annular cooling unit is arranged at the upper portion of the vacuum chamber, and a substrate holder made of a material with high thermal conductivity is arranged between the heating plate and cooling unit to be vertically movable (for example, see patent reference 1). When a substrate is heat-treated with this apparatus, the substrate holder on which the substrate is placed is moved downward. The lower surface of the substrate holder is brought into contact with the heating plate to heat the substrate through the substrate holder. After that, the substrate holder is moved upward to bring the periphery of the substrate holder into contact with the cooling unit, thereby cooling the substrate through the substrate holder. As an apparatus which heat-treats a substrate in non-contact with a heating plate, one is known which is provided with an airtight reaction chamber which heats the substrate at a high temperature, and a cooling portion (for example, see patent reference 2).    Patent Reference 1:    Japanese Patent Laid-Open No. 2003-318076    Patent Reference 2:    Japanese Patent Laid-Open No. 2005-299990